Input and runtime details for job 6860187 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase	_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@LB@
158	0.01775	0.3749	b1187	fadR	-13.89	0.045798	42 -- 66	152 -- 176	fatty acid metabolism regulon transcriptional regulator	_____________41________________________67\n_____________\|_________________________\|\n5'-AAA...CUUAA______G___G__GUG_________UUGAU...CAG-3'\n______________CGGUCA_GCA_GA___AGGCAAGUC\n______________\|:\|\|\|\|_:\|\|_\|\|___\|\|\|\|\|\|\|\|\|\n______________GUCAGU_UGU_CU___UCCGUUCAG\n3'-UUU...UAUGA______G___A__ACG_________UUGAA...UAG-5'\n_____________\|_________________________\|\n_____________177_______________________151\n	60 -- 66	152 -- 158	-31.5031 kcal/mol	7.04431 kcal/mol	8.02398 kcal/mol	41 67@LB@ \| \|@LB@5'-AAA...CUUAA G G GUG UUGAU...CAG-3'@LB@ CGGUCA GCA GA AGGCAAGUC@LB@ \|:\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ GUCAGU UGU CU UCCGUUCAG@LB@3'-UUU...UAUGA G A ACG UUGAA...UAG-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -13.89 kcal/mol@LB@Hybridization Energy -31.5031 kcal/mol@LB@Unfolding Energy - mRNA 7.04431 kcal/mol@LB@Unfolding Energy - sRNA 8.02398 kcal/mol@LB@@LB@Position - mRNA 42 -- 66@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 152 -- 158@LB@
58	0.005664	0.3247	b1878	flhE	-13.77	0.048330	266 -- 286	140 -- 162	proton seal during flagellar secretion	_____________265_____________________287\n_____________\|_______________________\|\n5'-CGU...AUGUG__________AGUGUA_______UACGC...AUC-3'\n______________GCAGGCAAGU________GGAAU\n______________\|\|\|\|\|\|\|\|\|\|________:\|\|\|\|\n______________CGUCCGUUCA________UCUUA\n3'-UUU...UACUA__________GUUGAAAG_____ACGCC...UAG-5'\n_____________\|_______________________\|\n_____________163_____________________139\n	269 -- 275	153 -- 159	-20.7539 kcal/mol	2.26514 kcal/mol	7.696 kcal/mol	265 287@LB@ \| \|@LB@5'-CGU...AUGUG AGUGUA UACGC...AUC-3'@LB@ GCAGGCAAGU GGAAU@LB@ \|\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ CGUCCGUUCA UCUUA@LB@3'-UUU...UACUA GUUGAAAG ACGCC...UAG-5'@LB@ \| \|@LB@ 163 139@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.7539 kcal/mol@LB@Unfolding Energy - mRNA 2.26514 kcal/mol@LB@Unfolding Energy - sRNA 7.696 kcal/mol@LB@@LB@Position - mRNA 266 -- 286@LB@Position - sRNA 140 -- 162@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 153 -- 159@LB@
37	0.00305	0.2773	b4084	alsK	-13.69	0.050122	28 -- 80	50 -- 101	D-allose kinase	_____________27__________________________________________________________81\n_____________\|___________________________________________________________\|\n5'-GCG...UACGA_____AG________G_________________________A__AAAAA___A_G____CAGGG...AAA-3'\n______________AAUUG__GU_GGACG_UU__CC__UGCAACCAG_GCAACUU_CG_____CUG_U_GCGG\n______________\|\|\|:\|__\|\|_\|\|\|\|\|_\|\|__\|\|__:\|\|\|\|\|\|\|\|_:\|\|\|\|\|\|_\|\|_____\|\|\|_\|_\|\|\|\|\n______________UUAGC__CA_CCUGC_AA__GG__GCGUUGGUC_UGUUGAA_GC_____GAC_A_CGCC\n3'-UUU...ACCAA_____AA__C_____G__UU__UU_________G____________________G____AUUUU...UAG-5'\n_____________\|___________________________________________________________\|\n_____________102_________________________________________________________49\n	56 -- 62	61 -- 67	-47.5504 kcal/mol	15.3524 kcal/mol	25.4279 kcal/mol	27 81@LB@ \| \|@LB@5'-GCG...UACGA AG G A AAAAA A G CAGGG...AAA-3'@LB@ AAUUG GU GGACG UU CC UGCAACCAG GCAACUU CG CUG U GCGG@LB@ \|\|\|:\| \|\| \|\|\|\|\| \|\| \|\| :\|\|\|\|\|\|\|\| :\|\|\|\|\|\| \|\| \|\|\| \| \|\|\|\|@LB@ UUAGC CA CCUGC AA GG GCGUUGGUC UGUUGAA GC GAC A CGCC@LB@3'-UUU...ACCAA AA C G UU UU G G AUUUU...UAG-5'@LB@ \| \|@LB@ 102 49@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -47.5504 kcal/mol@LB@Unfolding Energy - mRNA 15.3524 kcal/mol@LB@Unfolding Energy - sRNA 25.4279 kcal/mol@LB@@LB@Position - mRNA 28 -- 80@LB@Position - sRNA 50 -- 101@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 61 -- 67@LB@
167	0.01932	0.3812	b2912	fau	-13.57	0.053124	153 -- 189	109 -- 152	5-formyltetrahydrofolate cyclo-ligase family protein	_____________152__________190\n_____________\|____________\|\n5'-GAA...UGAGC____________GUCCG...UGG-3'\n______________AUGCUCGGUC_C\n______________\|\|:\|\|\|:\|\|\|_\|\n______________UAUGAGUCAG_G\n3'-UUU...GUGGU__________U_UGUAC...UAG-5'\n_____________\|____________\|\n_____________153__________108\n	31 -- 37	172 -- 178	-13.9133 kcal/mol	3.57919 kcal/mol	0.28482 kcal/mol	152 190@LB@ \| \|@LB@5'-GAA...UGAGC GUCCG...UGG-3'@LB@ AUGCUCGGUC C@LB@ \|\|:\|\|\|:\|\|\| \|@LB@ UAUGAGUCAG G@LB@3'-UUU...GUGGU U UGUAC...UAG-5'@LB@ \| \|@LB@ 153 108@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -13.9133 kcal/mol@LB@Unfolding Energy - mRNA 3.57919 kcal/mol@LB@Unfolding Energy - sRNA 0.28482 kcal/mol@LB@@LB@Position - mRNA 153 -- 189@LB@Position - sRNA 109 -- 152@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 172 -- 178@LB@
13	0.0007116	0.1842	b3052	hldE	-13.53	0.054228	111 -- 134	141 -- 169	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________110______________135\n_____________\|________________\|\n5'-GCG...CGUGA________________CUGGC...CGC-3'\n______________AC_UGGUGCGGGCAAG\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\|\|\n______________UG_ACUACGUCCGUUC\n3'-UUU...CAGUG__U_____________AGUUG...UAG-5'\n_____________\|________________\|\n_____________170______________140\n	119 -- 125	154 -- 160	-22.7709 kcal/mol	5.4675 kcal/mol	7.07904 kcal/mol	110 135@LB@ \| \|@LB@5'-GCG...CGUGA CUGGC...CGC-3'@LB@ AC UGGUGCGGGCAAG@LB@ \|\| \|\|:\|\|\|:\|\|\|\|\|\|@LB@ UG ACUACGUCCGUUC@LB@3'-UUU...CAGUG U AGUUG...UAG-5'@LB@ \| \|@LB@ 170 140@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.7709 kcal/mol@LB@Unfolding Energy - mRNA 5.4675 kcal/mol@LB@Unfolding Energy - sRNA 7.07904 kcal/mol@LB@@LB@Position - mRNA 111 -- 134@LB@Position - sRNA 141 -- 169@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 154 -- 160@LB@
83	0.008941	0.3575	b3343	tusB	-13.46	0.055944	1 -- 14	190 -- 203	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	______________1_____________15\n______________\|_____________\|\n___________5'-_______C______ACAUU...GCG-3'\n______________GCUGGCG_GUGAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________CGACCGC_CACUAA\n3'-UUU...UUAGA_______C______AAUGU...UAG-5'\n_____________\|______________\|\n_____________204____________189\n	1 -- 7	197 -- 203	-22.3351 kcal/mol	4.22102 kcal/mol	9.06745 kcal/mol	1 15@LB@ \| \|@LB@ 5'- C ACAUU...GCG-3'@LB@ GCUGGCG GUGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGACCGC CACUAA@LB@3'-UUU...UUAGA C AAUGU...UAG-5'@LB@ \| \|@LB@ 204 189@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -22.3351 kcal/mol@LB@Unfolding Energy - mRNA 4.22102 kcal/mol@LB@Unfolding Energy - sRNA 9.06745 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 190 -- 203@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 197 -- 203@LB@
73	0.007584	0.3458	b0059	rapA	-13.35	0.058963	263 -- 277	46 -- 60	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________262_____________278\n_____________\|_______________\|\n5'-GCU...GGAAC_______________UGCGC...UUU-3'\n______________CGUUGUCGCGGUGGA\n______________\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GCGACAGCGCCAUUU\n3'-UUU...UUGAA_______________UAUCA...UAG-5'\n_____________\|_______________\|\n_____________61______________45\n	269 -- 275	48 -- 54	-26.0749 kcal/mol	7.19742 kcal/mol	6.07408 kcal/mol	262 278@LB@ \| \|@LB@5'-GCU...GGAAC UGCGC...UUU-3'@LB@ CGUUGUCGCGGUGGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GCGACAGCGCCAUUU@LB@3'-UUU...UUGAA UAUCA...UAG-5'@LB@ \| \|@LB@ 61 45@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -26.0749 kcal/mol@LB@Unfolding Energy - mRNA 7.19742 kcal/mol@LB@Unfolding Energy - sRNA 6.07408 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 46 -- 60@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
114	0.01268	0.3575	b0888	trxB	-13.24	0.061992	5 -- 14	83 -- 92	thioredoxin reductase FAD/NAD(P)-binding	_____________4__________15\n_____________\|__________\|\n_______5'-AACA__________UUCAU...UGC-3'\n______________GGGGCGUUUA\n______________\|\|\|:\|\|:\|\|\|\n______________CCCUGCGAAU\n3'-UUU...CAACA__________UGGUU...UAG-5'\n_____________\|__________\|\n_____________93_________82\n	7 -- 13	84 -- 90	-15.9307 kcal/mol	0.512019 kcal/mol	6.69187 kcal/mol	4 15@LB@ \| \|@LB@ 5'-AACA UUCAU...UGC-3'@LB@ GGGGCGUUUA@LB@ \|\|\|:\|\|:\|\|\|@LB@ CCCUGCGAAU@LB@3'-UUU...CAACA UGGUU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -15.9307 kcal/mol@LB@Unfolding Energy - mRNA 0.512019 kcal/mol@LB@Unfolding Energy - sRNA 6.69187 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 84 -- 90@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease	_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching